monocle 1.6.2
Cole Trapnell
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/monocle | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings monocle_1.6.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/monocle.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monocle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monocle’ version ‘1.6.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘HSMMSingleCell’ ‘Biobase’ ‘ggplot2’ ‘splines’ ‘VGAM’ ‘igraph’ ‘plyr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘monocle’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘splines’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign_cell_lineage: no visible global function definition for ‘nei’
count_leaf_descendents: no visible global function definition for ‘nei’
estimateSizeFactorsForMatrix: no visible binding for global variable
‘median’
extract_fixed_ordering: no visible global function definition for ‘nei’
extract_good_branched_ordering: no visible binding for global variable
‘type’
extract_good_branched_ordering: no visible global function definition
for ‘nei’
extract_good_branched_ordering : extract_branched_ordering_helper: no
visible global function definition for ‘nei’
extract_good_branched_ordering : assign_cell_state_helper: no visible
global function definition for ‘nei’
extract_good_branched_ordering : assign_pseudotime_helper: no visible
global function definition for ‘nei’
extract_good_branched_ordering: no visible binding for global variable
‘pseudo_time’
extract_good_ordering: no visible global function definition for ‘nei’
extract_ordering: no visible global function definition for ‘nei’
get_next_node_id: no visible binding for '<<-' assignment to
‘next_node’
get_next_node_id: no visible binding for global variable ‘next_node’
make_canonical: no visible binding for global variable ‘type’
make_canonical: no visible global function definition for ‘nei’
measure_diameter_path: no visible global function definition for ‘nei’
orderCells: no visible binding for '<<-' assignment to ‘next_node’
parametricDispersionFit: no visible global function definition for
‘glm’
parametricDispersionFit: no visible global function definition for
‘Gamma’
parametricDispersionFit: no visible global function definition for
‘coefficients’
plot_genes_positive_cells: no visible binding for global variable
‘percent’
plot_genes_positive_cells: no visible global function definition for
‘geom_bar’
plot_spanning_tree: no visible binding for global variable
‘gene_short_name’
plot_spanning_tree: no visible global function definition for
‘geom_text’
plot_spanning_tree: no visible binding for global variable
‘sample_name’
pq_helper: no visible global function definition for
‘get.all.shortest.paths’
selectNegentropyGenes: no visible binding for global variable
‘log_expression’
selectNegentropyGenes: no visible global function definition for ‘vglm’
selectNegentropyGenes: no visible global function definition for
‘quantile’
Undefined global functions or variables:
Gamma coefficients gene_short_name geom_bar geom_text
get.all.shortest.paths glm log_expression median nei next_node
percent pseudo_time quantile sample_name type vglm
Consider adding
importFrom("stats", "Gamma", "coefficients", "glm", "median",
"quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/monocle.Rcheck/00check.log’
for details.
* installing *source* package ‘monocle’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: as.vector, unlist
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: as.vector, unlist
* DONE (monocle)